DOCSLIB.ORG

NER and HR Pathways Act Sequentially to Promote UV-C-Induced Germ Cell Apoptosis in Caenorhabditis Elegans

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
NER and HR Pathways Act Sequentially to Promote UV-C-Induced Germ Cell Apoptosis in Caenorhabditis Elegans Cell Death and Differentiation (2011) 18, 897–906 & 2011 Macmillan Publishers Limited All rights reserved 1350-9047/11 www.nature.com/cdd NER and HR pathways act sequentially to promote UV-C-induced germ cell apoptosis in Caenorhabditis elegans L Stergiou1,3,4, R Eberhard1,2,4, K Doukoumetzidis1 and MO Hengartner*,1 Ultraviolet (UV) radiation-induced DNA damage evokes a complex network of molecular responses, which culminate in DNA repair, cell cycle arrest and apoptosis. Here, we provide an in-depth characterization of the molecular pathway that mediates UV-C-induced apoptosis of meiotic germ cells in the nematode Caenorhabditis elegans. We show that UV-C-induced DNA lesions are not directly pro-apoptotic. Rather, they must first be recognized and processed by the nucleotide excision repair (NER) pathway. Our data suggest that NER pathway activity transforms some of these lesions into other types of DNA damage, which in turn are recognized and acted upon by the homologous recombination (HR) pathway. HR pathway activity is in turn required for the recruitment of the C. elegans homolog of the yeast Rad9-Hus1-Rad1 (9-1-1) complex and activation of downstream checkpoint kinases. Blocking either the NER or HR pathway abrogates checkpoint pathway activation and UV-C-induced apoptosis. Our results show that, following UV-C, multiple DNA repair pathways can cooperate to signal to the apoptotic machinery to eliminate potentially hazardous cells. Cell Death and Differentiation (2011) 18, 897–906; doi:10.1038/cdd.2010.158; published online 10 December 2010 Eukaryotic cells possess several surveillance mechanisms the signaling network that ultimately balances cellular DNA that, upon sensing DNA damage, initiate signaling cascades damage responses between genome maintenance, senes- that lead to response programs such as cell cycle arrest, DNA cence and death. Accordingly, loss of their function has repair and apoptosis, to protect the organism against the consequences for DNA repair, cellular proliferation and introduction of new mutations. Disruption of such pathways survival.6–8 results in increased genomic instability, a hallmark of most Simple model organisms are very useful to decipher types of cancers.1,2 complex DNA damage responses. In Caenorhabditis elegans, Genetic and biochemical studies have provided a thorough the effects of IR have been studied extensively.9,10 We mechanistic understanding of the various repair processes previously reported a genetic pathway that induces both initiated upon recognition of specific types of lesions. For apoptotic cell death of meiotic cells and cell cycle arrest of example, the nucleotide excision repair (NER) pathway proliferating mitotic cells following UV-C treatment.11 We removes cyclobutane pyrimidine dimers (CPDs) and 6-4 identified several new genes required for these responses and photoproducts generated upon exposure to ultraviolet (UV-C) genetically ordered them into a signaling pathway that light, whereas the homologous recombination (HR) machin- overlaps with, but is distinct from the pathway(s) activated ery repairs double-strand DNA breaks (DSBs) induced by upon IR. treatments such as ionizing radiation (IR).3 In this study, we investigate the molecular mechanism by Mutations in NER components underlie the syndromes which UV-C triggers apoptosis in the C. elegans adult xeroderma pigmentosum (XP), trichothiodystrophy or Cock- hermaphrodite germ line. We show that lesions caused by ayne syndrome. Patients are hypersensitive to sunlight and UV-C are not pro-apoptotic per se; rather, they first require exhibit a variety of clinical features, including developmental processing by the NER machinery before they can activate defects, predisposition to skin cancer or internal tumors, apoptosis. A fraction of UV-C lesions is likely transformed by neurological disorders and highly accelerated aging.4 Studies NER into DNA intermediates that are substrates for the HR in cell culture and mouse models,5,6 as well as in yeast have machinery. Activation of the latter, in turn, leads to recruitment led to the detailed molecular characterization of the NER of the C. elegans homolog of the yeast Rad9-Hus1-Rad1 factors.3 Besides repair, many of these factors participate in (9-1-1) complex, activation of downstream checkpoint kinases 1Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland and 2PhD Program in Molecular Life Sciences, Life Science Zurich Graduate School and MD/PhD Program, University of Zurich, Zurich, Switzerland *Corresponding author: MO Hengartner, Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland. Tel: þ 41 44 635 3140; Fax: þ 41 44 635 6861; E-mail: [email protected] 3Current address: Pike Pharma, Schlieren-Zurich, Switzerland. 4These authors contributed equally to this work. Keywords: apoptosis; C. elegans; HR; NER; UV-C Abbreviations: UV-C, ultraviolet light C (254 nm); IR, ionizing radiation; CPDs, cyclobutane pyrimidine dimers; DSB, double-strand DNA break; NER, nucleotide excision repair; HR, homologous recombination; 9-1-1 complex, Rad9-Hus1-Rad1 complex (HPR-9/HUS-1/MRT-2 in C. elegans); XPA, XPB, XPD, XPF, XPG, xeroderma pigmentosum complementation group A, B, D, F, G; RPA-1, replication protein A large subunit homolog in C. elegans Received 06.5.10; revised 07.9.10; accepted 20.9.10; Edited by E Baehrecke; published online 10.12.10 HR is required for UV-C-induced apoptosis in C. elegans L Stergiou et al 898 and initiation of p53-dependent apoptosis. Our results indicate rad-54(RNAi);spo-11(ok79) animals showed a greatly that UV-C-induced apoptosis in C. elegans requires the reduced response to IR and, surprisingly, also to UV sequential activation of at least two distinct DNA damage (Figure 1g). Importantly, spo-11(ok79) mutants respond response pathways. normally to both IR and UV, showing that the DNA damage response pathways are functional (Figure 1g). The HR pathway therefore plays an important role in promoting Results apoptosis in response to UV-C. Finally, we tested animals lacking the recombinase Components of the HR pathway are required for RAD-51. In the human and yeast homologs, RAD-51 acts UV-C-induced apoptosis. We previously showed that in downstream of MRE-11 and RAD-54 to promote strand C. elegans UV-C radiation induces cell cycle arrest in mitotic exchange during HR. rad-51(RNAi) animals also fail to germ cells and apoptosis of meiotic cells at the pachytene complete meiotic recombination, resulting in increased basal stage.11 We also reported that XPA-1 and XPC-1, two levels of apoptosis (Figure 1h). However, unlike in rad-54 components of the NER pathway, are required for the mutants, this increase can be suppressed only by activation of these responses, with XPA-1 acting upstream of atl-1(tm853), but not atm-1(gk186) (Supplementary Figure 2). the 9-1-1 complex protein HUS-1 and the p53 homolog In contrast to mre-11 and rad-54 mutants, rad-51(lf) CEP-1 in UV-induced apoptosis.11 animals did not show any defect in either UV- or IR-induced How does XPA-1 function promote p53 activation following apoptosis (Figure 1h).15 Moreover, UV-C treatment led to UV-C exposure? One possibility is that NER processes a RAD-51 foci formation (Supplementary Figure 3a), indepen- fraction of UV-C-induced damage into other types of DNA dent of both xpa-1 and rad-54 (Supplementary Figures 3b and structures, which might in turn activate apoptosis. Given our c). These observations suggest that UV-C-induced RAD-51 previous observation that many genes involved in response to foci formation and apoptosis are independent events, and that DSBs are also activated following UV-C, we focused our initial RAD-51 is not essential for UV-C-induced apoptosis. attention on the HR pathway. mre-11(ok179) mutants, which Taken together, our results support the idea that the lack the exonuclease responsible for the initial processing of proteins involved in early stages of HR also act to promote DSBs during meiosis, showed a compromised apoptotic apoptosis in response to UV-C damage. response to UV-C, suggesting a requirement for MRE-11 in the initiation of UV-C-induced apoptosis (Figure 1a). By The HR pathway acts downstream of the NER pathway to contrast, IR-induced apoptosis was only slightly reduced promote UV-C-induced apoptosis (Figure 1a), in agreement with previous reports,12 possibly owing to alternative processing pathways. The data above suggest that both NER and HR pathways are The homologs of RAD-54 and RAD-51 functionally interact required for UV-C-induced apoptosis. These two pathways during recombinational repair in yeasts and mammals.13,14 might act in parallel and be simultaneously required for the We analyzed two previously uncharacterized, likely null induction of apoptosis. Alternatively, they might act in succes- rad-54 mutants, tm1268 and ok615 (Supplementary Figure sion, with NER recognizing and processing the initial UV-C 1a). As homozygous rad-54 progeny from heterozygous lesions and HR relaying the signal to the apoptotic machinery. To mothers show fully penetrant maternal-effect lethality, we distinguish between these two possibilities, we determined the analyzed first-generation homozygotes for germline apopto- effect of mutations in the NER or HR pathways on the subcellular sis. Under normal growth conditions, both rad-54(ok615) and localization of selected DNA damage response proteins. rad-54(tm1268) mutants exhibit a strong increase in germline We started by examining the distribution of a functional apoptosis, an effect that could be phenocopied by RNAi RAD-54::YFP fusion protein (Supplementary Figure 1b). (Figure 1b). This increase was dependent on the endonu- RAD-54::YFP formed foci following exposure to both IR or clease SPO-11, which specifically generates the DSBs that UV-C, consistent with our observation that the HR pathway initiate meiotic recombination (Figure 1c),12 suggesting that participates in UV-C-induced responses (Figure 2a).
Load more

Recommended publications
  • XPB Induces C1D Expression to Counteract UV-Induced Apoptosis
    Published OnlineFirst June 8, 2010; DOI: 10.1158/1541-7786.MCR-09-0467 Molecular DNA Damage and Cellular Stress Responses Cancer Research XPB Induces C1D Expression to Counteract UV-Induced Apoptosis Guang Li1, Juhong Liu2, Mones Abu-Asab1, Shibuya Masabumi3, and Yoshiro Maru4 Abstract Although C1D has been shown to be involved in DNA double-strand break repair, how C1D expression was induced and the mechanism(s) by which C1D facilitates DNA repair in mammalian cells remain poorly understood. We and others have previously shown that expression of xeroderma pigmentosum B (XPB) pro- tein efficiently compensated the UV irradiation–sensitive phenotype of 27-1 cells, which lack functional XPB. To further explore XPB-regulated genes that could be involved in UV-induced DNA repair, differential dis- play analysis of mRNA levels from CHO-9, 27-1, and 27-1 complemented with wild-type XPB was done and C1D gene was identified as one of the major genes whose expression was significantly upregulated by restoring XPB function. We found that XPB is essential to induce C1D transcription after UV irradiation. The increase in C1D expression effectively compensates for the UV-induced proteolysis of C1D and thus maintains cellular C1D level to cope with DNA damage inflicted by UV irradiation. We further showed that although insufficient to rescue 27-1 cells from UV-induced apoptosis by itself, C1D facilitates XPB DNA repair through direct interaction with XPB. Our findings provided direct evidence that C1D is associated with DNA repair complex and may promote repair of UV-induced DNA damage. Mol Cancer Res; 8(6); 885–95.
    [Show full text]
  • Oncogenic H-Ras Up-Regulates Expression of ERCC1 to Protect Cells from Platinum-Based Anticancer Agents
    [CANCER RESEARCH 64, 4849–4857, July 15, 2004] Oncogenic H-Ras Up-Regulates Expression of ERCC1 to Protect Cells from Platinum-Based Anticancer Agents Cha-Kyung Youn,1 Mi-Hwa Kim,1 Hyun-Ju Cho,1 Hong-Beum Kim,1 In-Youb Chang,1 Myung-Hee Chung,3 and Ho Jin You1,2 1Research Center for Proteineous Materials and 2Department of Pharmacology, School of Medicine, Chosun University, Gwangju, and 3Department of Pharmacology, School of Medicine, Seoul National University, Seoul, Korea ABSTRACT elucidated, evidence suggests that the activated Ras may contribute to cisplatin resistance by stimulating the DNA repair activity (9, 12, 13). Tumors frequently contain mutations in the ras genes, resulting in the Hence, there has been considerable interest in determining which constitutive activation of the Ras-activated signaling pathway. The acti- vation of Ras is involved not only in tumor progression but also in the proteins mediate the altered DNA repair capacity in activated Ras- development of resistance of the tumor cells to platinum-based chemo- containing cells. However, the downstream target genes of the onco- therapeutic agents. To investigate the potential mechanisms underlying genic Ras, which are involved in the enhancement of the DNA repair this resistance, we analyzed the effect of activated H-Ras on the expression activity, are unclear. of the nucleotide excision repair genes. Here we identified ERCC1, which Cisplatin is one of the most effective and widely used anticancer is one of the key enzymes involved in nucleotide excision repair, as being drugs for treating human solid tumors (14). However, its therapeutic markedly up-regulated by the activated H-Ras.
    [Show full text]
  • Predictive Value of RAD51 on the Survival and Drug Responsiveness of Ovarian Cancer Yuchen Feng1, Daoqi Wang2, Luyang Xiong3, Guohua Zhen1 and Jiahong Tan4*
    Feng et al. Cancer Cell Int (2021) 21:249 https://doi.org/10.1186/s12935-021-01953-5 Cancer Cell International PRIMARY RESEARCH Open Access Predictive value of RAD51 on the survival and drug responsiveness of ovarian cancer Yuchen Feng1, Daoqi Wang2, Luyang Xiong3, Guohua Zhen1 and Jiahong Tan4* Abstract Background: Ovarian cancer has greatly endangered and deteriorated female health conditions worldwide. Refne- ment of predictive biomarkers could enable patient stratifcation and help optimize disease management. Methods: RAD51 expression profle, target-disease associations, and ftness scores of RAD51 were analyzed in ovar- ian cancer using bioinformatic analysis. To further identify its role, gene enrichment analysis was performed, and a regulatory network was constructed. Survival analysis and drug sensitivity assay were performed to evaluate the efect of RAD51 expression on ovarian cancer prognosis. The predictive value of RAD51 was then confrmed in a validation cohort immunohistochemically. Results: Ovarian cancer expressed more RAD51 than normal ovary. RAD51 conferred ovarian cancer dependency and was associated with ovarian cancer. RAD51 had extensive target-disease associations with various diseases, including ovarian cancer. Genes that correlate with and interact with RAD51 were involved in DNA damage repair and drug responsiveness. High RAD51 expression indicated unfavorable survival outcomes and resistance to platinum, taxane, and PARP inhibitors in ovarian cancer. In the validation cohort (126 patients), high RAD51 expression indicated platinum resistance, and platinum-resistant patients expressed more RAD51. Patients with high RAD51 expression had shorter OS (HR 2.968, P < 0.0001) and poorer PFS (HR 2.838, P < 0.0001). RAD51 expression level was negatively cor- related with patients’= survival length.
    [Show full text]
  • P38 MAPK-Mediated Activation of NF-Kb by the Rhogef Domain of Bcr
    Oncogene (2002) 21, 4601 – 4612 ª 2002 Nature Publishing Group All rights reserved 0950 – 9232/02 $25.00 www.nature.com/onc p38 MAPK-mediated activation of NF-kB by the RhoGEF domain of Bcr Malgorzata Korus1,2, Gwendolyn M Mahon1,2, Li Cheng1 and Ian P Whitehead*,1 1Department of Microbiology and Molecular Genetics, UMDNJ – New Jersey Medical School, Newark, New Jersey, NJ 07103, USA The oncogenic fusion protein p210 Bcr-Abl is causally et al., 1988; Fainstein et al., 1987; Konopka et al., associated with virtually all cases of chronic myelogenous 1984; Kurzrock et al., 1987; Walker et al., 1987). leukemia. The wild-type Bcr product has several Although animal models suggest that elevated levels of recognizable structural and functional motifs including Abl tyrosine kinase activity contribute to Bcr-Abl a domain that contains guanine nucleotide exchange mediated leukemogenesis (Lugo et al., 1990), the activity for Rho family GTPases (DH/PH domain). residues that distinguish the rearrangements associated Although this domain is retained within p210 Bcr-Abl, it with ALL (p185 Bcr-Abl) from the rearrangements has no known signaling activities in vivo. Here we report associated with CML (p210 Bcr-Abl) reside within the that a fragment of Bcr that encodes the isolated DH/PH Bcr protein. Thus, a complete understanding of the domain is a potent activator of the NF-kB transcription biological mechanisms that distinguish ALL from factor. Within the context of full length Bcr, this activity CML may depend upon the characterization of the is regulated by proximal flanking sequences that suppress signaling activities that reside within Bcr.
    [Show full text]
  • The Bloom Syndrome Protein Limits the Lethality Associated with RAD51 Deficiency
    Published OnlineFirst March 9, 2010; DOI: 10.1158/1541-7786.MCR-09-0534 Molecular DNA Damage and Cellular Stress Responses Cancer Research The Bloom Syndrome Protein Limits the Lethality Associated with RAD51 Deficiency Kenza Lahkim Bennani-Belhaj1,2, Sébastien Rouzeau1,2, Géraldine Buhagiar-Labarchède1,2, Pauline Chabosseau1,2, Rosine Onclercq-Delic1,2, Emilie Bayart1, Fabrice Cordelières3,4, Jérôme Couturier5,6, and Mounira Amor-Guéret1,2 Abstract Little is known about the functional interaction between the Bloom's syndrome protein (BLM) and the re- combinase RAD51 within cells. Using RNA interference technology, we provide the first demonstration that RAD51 acts upstream from BLM to prevent anaphase bridge formation. RAD51 downregulation was associated with an increase in the frequency of BLM-positive anaphase bridges, but not of BLM-associated ultrafine bridges. Time-lapse live microscopy analysis of anaphase bridge cells revealed that BLM promoted cell survival in the absence of Rad51. Our results directly implicate BLM in limiting the lethality associated with RAD51 deficiency through the processing of anaphase bridges resulting from the RAD51 defect. These findings provide insight into the molecular basis of some cancers possibly associated with variants of the RAD51 gene family. Mol Cancer Res; 8(3); 385–94. ©2010 AACR. Introduction cently, SUMOylation of BLM has been shown to regulate its association with RAD51 and its function in HR-medi- Bloom's syndrome displays one of the strongest known ated repair of damaged replication forks (13). In several correlations between chromosomal instability and a high models, it has been proposed that BLM restarts replication risk of cancer at an early age.
    [Show full text]
  • Mutations in the RAD54 Recombination Gene in Primary Cancers
    Oncogene (1999) 18, 3427 ± 3430 ã 1999 Stockton Press All rights reserved 0950 ± 9232/99 $12.00 http://www.stockton-press.co.uk/onc SHORT REPORT Mutations in the RAD54 recombination gene in primary cancers Masahiro Matsuda1,4, Kiyoshi Miyagawa*,1,2, Mamoru Takahashi2,4, Toshikatsu Fukuda1,4, Tsuyoshi Kataoka4, Toshimasa Asahara4, Hiroki Inui5, Masahiro Watatani5, Masayuki Yasutomi5, Nanao Kamada3, Kiyohiko Dohi4 and Kenji Kamiya2 1Department of Molecular Pathology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Hiroshima 734, Japan; 2Department of Developmental Biology and Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Hiroshima 734, Japan; 3Department of Cancer Cytogenetics, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Hiroshima 734, Japan; 42nd Department of Surgery, Hiroshima University School of Medicine, 1-2-3 Kasumi, Minami-ku, Hiroshima 734, Japan; 51st Department of Surgery, Kinki University School of Medicine, 377-2 Ohno-higashi, Osaka-sayama, Osaka 589, Japan Association of a recombinational repair protein RAD51 therefore, probable that members of the RAD52 with tumor suppressors BRCA1 and BRCA2 suggests epistasis group are altered in cancer. that defects in homologous recombination are responsible To investigate whether RAD54, a member of the for tumor formation. Also recent ®ndings that a protein RAD52 epistasis group, is mutated in human cancer, associated with the MRE11/RAD50 repair complex is we performed SSCP analysis and direct sequencing of mutated in Nijmegen breakage syndrome characterized PCR products using mRNAs from 132 unselected by increased cancer incidence and ionizing radiation primary tumors including 95 breast cancers, 13 sensitivity strongly support this idea.
    [Show full text]
  • Scaffolding Protein SPIDR/KIAA0146 Connects the Bloom Syndrome Helicase with Homologous Recombination Repair
    Scaffolding protein SPIDR/KIAA0146 connects the Bloom syndrome helicase with homologous recombination repair Li Wan1, Jinhua Han1, Ting Liu1, Shunli Dong, Feng Xie, Hongxia Chen, and Jun Huang2 Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China Edited by James E. Cleaver, University of California, San Francisco, CA, and approved February 26, 2013 (received for review December 1, 2012) The Bloom syndrome gene product, BLM, is a member of the highly of the SDSA pathway (6, 7). The ability of BLM to yield non- conserved RecQ family. An emerging concept is the BLM helicase crossover products is thought to play a critical role in the avoidance collaborates with the homologous recombination (HR) machinery to of chromosomal rearrangements during the homolog-directed re- help avoid undesirable HR events and to achieve a high degree of pair of chromosomal lesions. As a result, cells defective for BLM fidelity during the HR reaction. However, exactly how such coordina- exhibit elevated rates of sister chromatid exchange (SCE) (19–21). tion occurs in vivo is poorly understood. Here, we identified a protein Upon the occurrence of DNA damage, BLM is able to form termed SPIDR (scaffolding protein involved in DNA repair) as the link discrete foci, where it colocalizes with other DNA repair proteins between BLM and the HR machinery. SPIDR independently interacts (22, 23). However, mechanistically how BLM is recruited to sites with BLM and RAD51 and promotes the formation of a BLM/RAD51- of DNA damage and how it collaborates with other proteins to containing complex of biological importance. Consistent with its role mediate recombination repair remain largely unexplored.
    [Show full text]
  • Ras/Raf/MEK/ERK and PI3K/PTEN/Akt/Mtor Cascade Inhibitors: How Mutations Can Result in Therapy Resistance and How to Overcome Resistance
    www.impactjournals.com/oncotarget/ Oncotarget, October, Vol.3, No 10 Ras/Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR Cascade Inhibitors: How Mutations Can Result in Therapy Resistance and How to Overcome Resistance James A. McCubrey1, Linda S. Steelman1, William H. Chappell1, Stephen L. Abrams1, Richard A. Franklin1, Giuseppe Montalto2, Melchiorre Cervello3, Massimo Libra4, Saverio Candido4, Grazia Malaponte4, Maria C. Mazzarino4, Paolo Fagone4, Ferdinando Nicoletti4, Jörg Bäsecke5, Sanja Mijatovic6, Danijela Maksimovic- Ivanic6, Michele Milella7, Agostino Tafuri8, Francesca Chiarini9, Camilla Evangelisti9, Lucio Cocco10, Alberto M. Martelli9,10 1 Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, NC, USA 2 Department of Internal Medicine and Specialties, University of Palermo, Palermo, Italy 3 Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare “Alberto Monroy”, Palermo, Italy 4 Department of Bio-Medical Sciences, University of Catania, Catania, Italy 5 Department of Medicine, University of Göttingen, Göttingen, Germany 6 Department of Immunology, Instititue for Biological Research “Sinisa Stankovic”, University of Belgrade, Belgrade, Serbia 7 Regina Elena National Cancer Institute, Rome, Italy 8 Sapienza, University of Rome, Department of Cellular Biotechnology and Hematology, Rome, Italy 9 Institute of Molecular Genetics, National Research Council-Rizzoli Orthopedic Institute, Bologna, Italy. 10 Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy Correspondence to: James A. McCubrey, email: [email protected] Keywords: Targeted Therapy, Therapy Resistance, Cancer Stem Cells, Raf, Akt, PI3K, mTOR Received: September 12, 2012, Accepted: October 18, 2012, Published: October 20, 2012 Copyright: © McCubrey et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
    [Show full text]
  • Discovery of the Essential Roles of CRK9 in Gene Expression and Of
    University of Connecticut OpenCommons@UConn Doctoral Dissertations University of Connecticut Graduate School 5-27-2015 Lessons from Trypanosome TFIIH: Discovery of the Essential Roles of CRK9 in Gene Expression and of the Divergent Helicase Paralog XPB-R in Nucleotide Excision Repair Nitika Badjatia University of Connecticut - Storrs, [email protected] Follow this and additional works at: https://opencommons.uconn.edu/dissertations Recommended Citation Badjatia, Nitika, "Lessons from Trypanosome TFIIH: Discovery of the Essential Roles of CRK9 in Gene Expression and of the Divergent Helicase Paralog XPB-R in Nucleotide Excision Repair" (2015). Doctoral Dissertations. 866. https://opencommons.uconn.edu/dissertations/866 Lessons from Trypanosome TFIIH: Discovery of the Essential Roles of CRK9 in Gene Expression and of the Divergent Helicase Paralog XPB-R in Nucleotide Excision Repair Nitika Badjatia University of Connecticut, [2015] Eukaryotic TFIIH consists of a core of seven subunits, including the DNA helicase Xeroderma Pigmentosum B (XPB), and a cyclin-dependent kinase (CDK)-activating complex (CAK) that contains CDK7. XPB is crucial for DNA unwinding during transcription and nucleotide excision repair (NER) while the CAK complex phosphorylates RNA polymerase II (RNAPII) carboxy terminal domain (CTD), enabling the enzyme’s promoter clearance. Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp. are lethal human parasites, belonging to the early-diverged order Kinetoplastida. They transcribe genes polycistronically and require spliced leader (SL) trans splicing for the maturation of mRNAs from polycistronic precursors. SL RNA gene (SLRNA) transcription by RNAPII depends on trypanosome TFIIH complex which contains orthologs of all core subunits but lacks the CAK complex. Despite this, the trypanosome CTD is phosphorylated and essential for SLRNA transcription.
    [Show full text]
  • Melanomas Are Comprised of Multiple Biologically Distinct Categories
    Melanomas are comprised of multiple biologically distinct categories, which differ in cell of origin, age of onset, clinical and histologic presentation, pattern of metastasis, ethnic distribution, causative role of UV radiation, predisposing germ line alterations, mutational processes, and patterns of somatic mutations. Neoplasms are initiated by gain of function mutations in one of several primary oncogenes, typically leading to benign melanocytic nevi with characteristic histologic features. The progression of nevi is restrained by multiple tumor suppressive mechanisms. Secondary genetic alterations override these barriers and promote intermediate or overtly malignant tumors along distinct progression trajectories. The current knowledge about pathogenesis, clinical, histological and genetic features of primary melanocytic neoplasms is reviewed and integrated into a taxonomic framework. THE MOLECULAR PATHOLOGY OF MELANOMA: AN INTEGRATED TAXONOMY OF MELANOCYTIC NEOPLASIA Boris C. Bastian Corresponding Author: Boris C. Bastian, M.D. Ph.D. Gerson & Barbara Bass Bakar Distinguished Professor of Cancer Biology Departments of Dermatology and Pathology University of California, San Francisco UCSF Cardiovascular Research Institute 555 Mission Bay Blvd South Box 3118, Room 252K San Francisco, CA 94158-9001 [email protected] Key words: Genetics Pathogenesis Classification Mutation Nevi Table of Contents Molecular pathogenesis of melanocytic neoplasia .................................................... 1 Classification of melanocytic neoplasms
    [Show full text]
  • University of Florida Thesis Or Dissertation Formatting
    AAA ATPASE CDC48A AND ITS ASSOCIATION WITH UBIQUITIN-LIKE SAMP1 AND DNA REPAIR IN ARCHAEA By SWATHI DANTULURI A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2018 © 2018 Swathi Dantuluri I dedicate this to my family and friends for their endless love, support and company.Everybody who has taken the time and energy to teach me everything small or big. ACKNOWLEDGMENTS During my graduate career at the University of Florida, there are many people to whom I will be eternally indebted to for supporting and advising me along the way. Firstly, I would like to thank my advisor, Dr. Julie A. Maupin-Furlow for providing me the opportunity to work under her guidance as well as for all her help, advice, support, and encouragement throughout my time in her lab. I would also like to thank my committee members Dr. Sixue Chen, Dr.Tony Romeo and Dr. Nemat.O.Keyhani for their constructive advice and guidance. I must also express my gratitude to all the past and current Maupin lab members with whom I developed a warm and friendly working relationship over time, especially Dr. Nathaniel Hepowit who patiently taught me all the lab techniques, Dr. Xian Fu, Dr. Lana J. McMillan, Dr. Shiyun Cao, Dr. Sungmin Hwang, Zachary Adams, Cuper Ramirez, Paula Mondragon, and Jou Chin Chan. I also would like to thank all the undergraduate researchers in our lab for their dedication: Shae Marguiles, Sonam Parag, Gayathri Srinivasan, and Whinkie Leung.
    [Show full text]
  • Genome-Wide Discovery of G-Quadruplexes in Barley
    www.nature.com/scientificreports OPEN Genome‑wide discovery of G‑quadruplexes in barley H. Busra Cagirici1, Hikmet Budak2,3 & Taner Z. Sen1* G‑quadruplexes (G4s) are four‑stranded nucleic acid structures with closely spaced guanine bases forming square planar G‑quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome‑wide identifcation of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5′ untranslated region (5′ UTR), the frst coding domain sequence, and the frst intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs. DNA and RNA sequences ofen form functional secondary structures, such as loops, hairpins, duplexes, triplexes, and quadruplexes1,2. G-quadruplexes (G4) are four-stranded nucleic acid structures formed within guanine (G) rich sequences. Consecutive G bases form G-stems (also called G-islands3 or G-runs4), which make up one strand of a G4 structure.
    [Show full text]